Sample QC: Difference between revisions
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Al Forrest (talk | contribs) (Created page with 'Checking clustering of replicates, expression of biomarkers, mapped tag count, promoter hit rate, RIN score. '''Library depth check'''media:Less_than_500000_Q20tags.xls …') |
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'''Library depth check'''[[media:Less_than_500000_Q20tags.xls]] |
'''Library depth check''' - [[media:Less_than_500000_Q20tags.xls]] |
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Human samples with less than 500,000 Q20 mapped tags = '''88'''<br> |
Human samples with less than 500,000 Q20 mapped tags = '''88'''<br> |
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'''Promoter hit rate (only for samples in release 12 so far)''' [[media:Less_than_50percent_promoter_rate.xls]] |
'''Promoter hit rate (only for samples in release 12 so far)''' - [[media:Less_than_50percent_promoter_rate.xls]] |
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Human samples with less than 50% = 30 12 post mortem tissue samples from Kere lab (RNA was degraded) 4 commercial post mortem tissue samples (RNA looks ok) 3 macrophage samples from Hume Lab 2 Saos samples from Summers Lab 3 neuron/neural stem cells – suspect this is biology |
Human samples with less than 50% = 30 12 post mortem tissue samples from Kere lab (RNA was degraded) 4 commercial post mortem tissue samples (RNA looks ok) 3 macrophage samples from Hume Lab 2 Saos samples from Summers Lab 3 neuron/neural stem cells – suspect this is biology |
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Revision as of 16:00, 24 November 2011
Checking clustering of replicates, expression of biomarkers, mapped tag count, promoter hit rate, RIN score.
Library depth check - media:Less_than_500000_Q20tags.xls
Human samples with less than 500,000 Q20 mapped tags = 88
- 18 macrophage samples from Hume Lab
- 4 MSC adipo samples from Arner Lab
- 23 K562 samples from Klinken Lab
- 10 CMP/GMP/PMN samples from Lenarrtson Lab
- 3 from Khachigian lab
- 23 commercial primary cells
Mouse samples with less than 500,000 Q20 mapped tags = 11
- 4 J2E samples from Klinken lab
- 3 commercial primary cells
Promoter hit rate (only for samples in release 12 so far) - media:Less_than_50percent_promoter_rate.xls
Human samples with less than 50% = 30 12 post mortem tissue samples from Kere lab (RNA was degraded) 4 commercial post mortem tissue samples (RNA looks ok) 3 macrophage samples from Hume Lab 2 Saos samples from Summers Lab 3 neuron/neural stem cells – suspect this is biology
